jvarkit

HaploGroupCaseControl

Run Fisher test for Haplogroup input.

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar haplogroupcasectrl  [options] Files

Usage: haplogroupcasectrl [options] Files
  Options:
    --cases
      File or comma-separated list of control samples
    --controls
      File or comma-separated list of control samples
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --phylotree, --tree
      Path/URL to a valid XML formatted phylotree ( 
      https://github.com/genepi/phylotree-rcrs-17 ).
      Default: https://raw.githubusercontent.com/genepi/phylotree-rcrs-17/main/src/tree.xml
    --version
      print version and exit

Keywords

• haplogroup
• burden
• mitochondrial

Creation Date

20240610

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/haplogroupcasectrl/HaploGroupCaseControl.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite haplogroupcasectrl ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Examples

 java -jar jvarkit.jar haplogroupcasectrl --cases input.cases  --controls input.ctrls  --tree input.xml   input.tsv

Examples

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